Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 77 of 208
Found at i:22582581 original size:3 final size:3
Alignment explanation
Indices: 22582573--22582609 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
22582563 TTCATTTTAT
22582573 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22582610 AAGAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22583649 original size:19 final size:21
Alignment explanation
Indices: 22583627--22583666 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
22583617 ATATATTTTT
22583627 TATTTTTT-TATTT-TTAAAA
1 TATTTTTTGTATTTATTAAAA
22583646 TATTTTTTGTATTTATTAAAA
1 TATTTTTTGTATTTATTAAAA
22583667 ATCGGGCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TATTTTTTGTATTTATTAAAA
Found at i:22590878 original size:15 final size:15
Alignment explanation
Indices: 22590853--22590887 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22590843 GACTCTATTT
*
22590853 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
22590867 TAATTAATATTAAGA
1 TAATTAATATTAAGA
22590882 TAATTA
1 TAATTA
22590888 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:22594248 original size:46 final size:46
Alignment explanation
Indices: 22594181--22594273 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
22594171 TGAGTTAGGT
22594181 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
1 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
22594227 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
1 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
22594273 T
1 T
22594274 GATACAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (46 bp):
TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
Found at i:22595490 original size:22 final size:23
Alignment explanation
Indices: 22595448--22595496 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
22595438 TCAAATTAAT
22595448 ATATTAATATATGAATATATGA-
1 ATATTAATATATGAATATATGAC
* *
22595470 ATATT-ATATTTGGATATTATGAC
1 ATATTAATATATGAATA-TATGAC
22595493 ATAT
1 ATAT
22595497 AAACTAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 10 0.43
23 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (23 bp):
ATATTAATATATGAATATATGAC
Found at i:22595768 original size:17 final size:18
Alignment explanation
Indices: 22595743--22595788 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
22595733 TATAAGAATA
*
22595743 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
22595760 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
22595778 ATTAAATTATA
1 ATTAAATTATA
22595789 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:22596008 original size:44 final size:45
Alignment explanation
Indices: 22595945--22596038 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
22595935 TATTACAATA
22595945 TCATTCCATTCAACCAAACACA-AGAA-TACCATTACAGTTCTATT
1 TCATTCCATTCAACCAAACA-ATAGAATTACCATTACAGTTCTATT
* *
22595989 TCATTCCATTCAACCAAACAATTGAATTACTATTACAGTTCTATT
1 TCATTCCATTCAACCAAACAATAGAATTACCATTACAGTTCTATT
*
22596034 CCATT
1 TCATT
22596039 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (45 bp):
TCATTCCATTCAACCAAACAATAGAATTACCATTACAGTTCTATT
Found at i:22596041 original size:16 final size:16
Alignment explanation
Indices: 22596020--22596091 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
22596010 TTGAATTACT
*
22596020 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
22596036 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
*
22596052 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
22596068 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
22596084 ATTACAGC
1 ATTACAGC
22596092 GAACCAAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:22596388 original size:31 final size:32
Alignment explanation
Indices: 22596323--22596388 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
22596313 GTTAACTAAA
22596323 ATTGTTTAAATAATAATTTAAAAGTTAAAAAT
1 ATTGTTTAAATAATAATTTAAAAGTTAAAAAT
*
22596355 ATTG-TTAAAT-AT-ATTTAACAATTTAAAACAT
1 ATTGTTTAAATAATAATTTAA-AAGTTAAAA-AT
22596386 ATT
1 ATT
22596389 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 6 0.19
30 10 0.32
31 11 0.35
32 4 0.13
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (32 bp):
ATTGTTTAAATAATAATTTAAAAGTTAAAAAT
Found at i:22601078 original size:199 final size:201
Alignment explanation
Indices: 22600738--22601137 Score: 759
Period size: 199 Copynumber: 2.0 Consensus size: 201
22600728 TTTAAATGGT
22600738 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
*
22600803 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAGTAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
22600868 AACTATAATGTTTTAAGTTCAAACCAATGTGT-A-TTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
22600931 GAACTC
196 GAACTC
*
22600937 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAATA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
22601002 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
*
22601067 AACTATAATGTTTTAAGTTCAAATCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
22601132 GAACTC
196 GAACTC
22601138 TCTCAAAATA
Statistics
Matches: 196, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
199 159 0.81
200 1 0.01
201 36 0.18
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (201 bp):
GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
GAACTC
Found at i:22601458 original size:26 final size:27
Alignment explanation
Indices: 22601417--22601469 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
22601407 TGAAAATAGA
* *
22601417 AAAAATACAATTGGAAAAA-TAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
22601443 AAAAATAAAATAGGAAAAAGTAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
22601470 TTATATGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (27 bp):
AAAAATAAAATAGGAAAAAGTAGGAAG
Found at i:22603284 original size:62 final size:64
Alignment explanation
Indices: 22603187--22603312 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 64
22603177 AATTTCCTAG
**
22603187 AATTCTTAACGATTAGAAGATATTTGCGTATGGTGTACCAATTAATAAGCTTAA-G-GTGTTAT
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
*
22603249 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATGAGCTTAATGAGTGTTAT
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
22603313 GTTAAATGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 51 0.86
63 1 0.02
64 7 0.12
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (64 bp):
AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
Found at i:22605674 original size:23 final size:23
Alignment explanation
Indices: 22605643--22605688 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
22605633 TTATTAACAT
* *
22605643 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATATTCGATTAA
*
22605666 TGTTTGTGAACATATTCGATTAA
1 TGTTCGTGAACATATTCGATTAA
22605689 GTTAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATATTCGATTAA
Found at i:22608192 original size:22 final size:22
Alignment explanation
Indices: 22608162--22608211 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
22608152 AATATTTAAA
* *
22608162 ATTATAAAAAAATCATAAAAGT
1 ATTAAAAAAAAATCATAAAAAT
* **
22608184 ATTAAAAAAATATTTTAAAAAT
1 ATTAAAAAAAAATCATAAAAAT
22608206 ATTAAA
1 ATTAAA
22608212 CATATTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
ATTAAAAAAAAATCATAAAAAT
Found at i:22609505 original size:21 final size:21
Alignment explanation
Indices: 22609478--22609531 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
22609468 TATTAAATCA
22609478 TTATAATATTTTAC-ATTTTT
1 TTATAATATTTTACAATTTTT
22609498 TTAATAAT-TGTTTACAATTTTT
1 TT-ATAATAT-TTTACAATTTTT
22609520 TTATAA-ATTTTA
1 TTATAATATTTTA
22609532 TAGCTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 7 0.23
21 15 0.50
22 8 0.27
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATAATATTTTACAATTTTT
Found at i:22613115 original size:15 final size:15
Alignment explanation
Indices: 22613097--22613128 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22613087 CATTTCACTA
*
22613097 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
22613112 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
22613127 TT
1 TT
22613129 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:22632276 original size:35 final size:35
Alignment explanation
Indices: 22632210--22632297 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
22632200 GTACACGGTT
* *
22632210 AACCATCCAGCACACCAG-ATGCTCAAGTGAGCCA
1 AACCAACCAACACACCAGAATGCTCAAGTGAGCCA
* *
22632244 GACCAACCAACACACCAGAATGCTCGTA-TGAGCCA
1 AACCAACCAACACACCAGAATGCTC-AAGTGAGCCA
22632279 AACCAACCAACACACCAGA
1 AACCAACCAACACACCAGA
22632298 GTACACTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 15 0.32
35 31 0.66
36 1 0.02
ACGTcount: A:0.40, C:0.36, G:0.15, T:0.09
Consensus pattern (35 bp):
AACCAACCAACACACCAGAATGCTCAAGTGAGCCA
Found at i:22635943 original size:13 final size:13
Alignment explanation
Indices: 22635925--22635950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22635915 CCCATGTGAA
22635925 CTTAGTAAAAGGT
1 CTTAGTAAAAGGT
22635938 CTTAGTAAAAGGT
1 CTTAGTAAAAGGT
22635951 TAGAGTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CTTAGTAAAAGGT
Found at i:22642961 original size:22 final size:22
Alignment explanation
Indices: 22642933--22642988 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
22642923 CTGGAGTTCG
22642933 CAGAGAATGTCAATACTAGGGA
1 CAGAGAATGTCAATACTAGGGA
* * *
22642955 CAGAGAATGTCAGTACTGGGGG
1 CAGAGAATGTCAATACTAGGGA
*
22642977 CAGCGAA-GTCAA
1 CAGAGAATGTCAA
22642989 GAAAAAATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (22 bp):
CAGAGAATGTCAATACTAGGGA
Found at i:22646022 original size:23 final size:23
Alignment explanation
Indices: 22645912--22646026 Score: 140
Period size: 23 Copynumber: 4.9 Consensus size: 23
22645902 CGTCATTGGA
*
22645912 AAAGGATGAATTGACAGAAATGT
1 AAAGGATGAATTGACGGAAATGT
*
22645935 AAAGGATGAATTGACGAAAAATGT
1 AAAGGATGAATTGACG-GAAATGT
* * * *
22645959 AAAGGAGGAACTGATGAAAATGT
1 AAAGGATGAATTGACGGAAATGT
*
22645982 AAAGGATGAATTGACGGTAATGT
1 AAAGGATGAATTGACGGAAATGT
*
22646005 AAAGGATGAATTGGCGGTAAAT
1 AAAGGATGAATTGACGG-AAAT
22646027 TATCTGAGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
23 56 0.72
24 22 0.28
ACGTcount: A:0.45, C:0.04, G:0.29, T:0.22
Consensus pattern (23 bp):
AAAGGATGAATTGACGGAAATGT
Found at i:22653498 original size:23 final size:23
Alignment explanation
Indices: 22653468--22653571 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
22653458 ATTGGGAAAT
22653468 GATGAATTGACGAAAATGTAAAG
1 GATGAATTGACGAAAATGTAAAG
*
22653491 GATGAATTGACGAAAAATGTAAAT
1 GATGAATTGACG-AAAATGTAAAG
* * **
22653515 GAGGAACTGGTGGAAAATGTAAAG
1 GATGAA-TTGACGAAAATGTAAAG
* *
22653539 GATGAATCGAC-AGTAATGTAAAG
1 GATGAATTGACGA-AAATGTAAAG
22653562 GATGAATTGA
1 GATGAATTGA
22653572 AGGCAAATTG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.02
23 32 0.48
24 30 0.45
25 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.22
Consensus pattern (23 bp):
GATGAATTGACGAAAATGTAAAG
Found at i:22653512 original size:24 final size:24
Alignment explanation
Indices: 22653468--22653571 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
22653458 ATTGGGAAAT
22653468 GATGAATTGACG-AAAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
*
22653491 GATGAATTGACGAAAAATGTAAAT
1 GATGAATTGACGAAAAATGTAAAG
* * ** *
22653515 GAGGAACTGGTGGAAAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
* **
22653539 GATGAATCGAC-AGTAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
22653562 GATGAATTGA
1 GATGAATTGA
22653572 AGGCAAATTG
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
23 30 0.47
24 34 0.53
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.22
Consensus pattern (24 bp):
GATGAATTGACGAAAAATGTAAAG
Found at i:22655017 original size:29 final size:29
Alignment explanation
Indices: 22654975--22655031 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
22654965 GTTATGGGTG
*
22654975 TAAAGTCTGGTAATGCTTCGTAAAGTCTA
1 TAAAATCTGGTAATGCTTCGTAAAGTCTA
22655004 TAAAATCTGGTAATGCTTCGTAAAGTCT
1 TAAAATCTGGTAATGCTTCGTAAAGTCT
22655032 GTAATGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (29 bp):
TAAAATCTGGTAATGCTTCGTAAAGTCTA
Found at i:22664966 original size:91 final size:89
Alignment explanation
Indices: 22664858--22665031 Score: 258
Period size: 91 Copynumber: 1.9 Consensus size: 89
22664848 TATCCATGAG
* * * *
22664858 TTACTGGTAGCTTTTATCTGCAAACCCATTGTGTATTCACAACTACTGGTAGCATATTAACTTGC
1 TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTA-TGGCAGCATATTAACCTGC
* *
22664923 AAACACTAGTGGTTTATCCACAATTT
65 -AACACTAGTGATTCATCCACAATTT
* *
22664949 TTACTGGCAACTTTTATCTGCAAACCCGTTGTGTATTCACAACTATTGCAGCATATTAACCTGCA
1 TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTATGGCAGCATATTAACCTGCA
22665014 ACACTAGTGATTCATCCA
66 ACACTAGTGATTCATCCA
22665032 TGAACTAGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 17 0.23
90 16 0.21
91 42 0.56
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (89 bp):
TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTATGGCAGCATATTAACCTGCA
ACACTAGTGATTCATCCACAATTT
Found at i:22670594 original size:25 final size:25
Alignment explanation
Indices: 22670558--22670715 Score: 101
Period size: 25 Copynumber: 6.4 Consensus size: 25
22670548 GCTCTCTCTC
*
22670558 GAGCCATATAACAGGAAGCTCATAT
1 GAGCCATATAACAGGAAGCTCATAA
* * * **
22670583 GAGCCATGTAACGGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATAA
* ** *
22670608 GGGCTGTATAACGGGAAGCTCATAA
1 GAGCCATATAACAGGAAGCTCATAA
* **
22670633 GAGCCATA-ATCAGGAAGCTCATGG
1 GAGCCATATAACAGGAAGCTCATAA
*
22670657 GAGCCA-ATAACAGGTAGCTC-TGAA
1 GAGCCATATAACAGGAAGCTCAT-AA
* *
22670681 GAGTCAT-TAATTAGGAAGCTCCA-AA
1 GAGCCATATAA-CAGGAAGCT-CATAA
*
22670706 TAGCCATATA
1 GAGCCATATA
22670716 CCGGGAAGTT
Statistics
Matches: 98, Mismatches: 28, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
23 2 0.02
24 36 0.37
25 57 0.58
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAA
Found at i:22670652 original size:24 final size:24
Alignment explanation
Indices: 22670621--22670834 Score: 82
Period size: 25 Copynumber: 8.7 Consensus size: 24
22670611 CTGTATAACG
22670621 GGAAGCTCATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
**
22670645 GGAAGCTCATGGGAGCCAATAA-CA
1 GGAAGCTCATAAGAGCC-ATAATCA
* * *
22670669 GGTAGCTC-TGAAGAGTCATTAATTA
1 GGAAGCTCAT-AAGAGCCA-TAATCA
* * *
22670694 GGAAGCTCCA-AATAGCCATATACCG
1 GGAAGCT-CATAAGAGCCATA-ATCA
* * *
22670719 GGAAGTTCA-AGCGAGCCAT-ATCG
1 GGAAGCTCATA-AGAGCCATAATCA
* ** *
22670742 GGAAACTTC-GGAGAGCCATTAATCT
1 GGAAGC-TCATAAGAGCCA-TAATCA
* * *
22670767 GGAAGCTCACAAAGGGCCTTTAATCA
1 GGAAGCTCA-TAAGAGCC-ATAATCA
* *
22670793 GGAAGCTCACGAAGAGCCATATATCG
1 GGAAGCTCA-TAAGAGCCATA-ATCA
22670819 GGACA-CTCATAAGAGC
1 GGA-AGCTCATAAGAGC
22670835 TGTTATGTGT
Statistics
Matches: 140, Mismatches: 33, Indels: 33
0.68 0.16 0.16
Matches are distributed among these distances:
23 15 0.11
24 41 0.29
25 46 0.33
26 37 0.26
27 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:22671828 original size:5 final size:5
Alignment explanation
Indices: 22671818--22671846 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
22671808 TATATGATGA
22671818 TATTT TATTT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATT
22671847 ATTTATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:22673300 original size:6 final size:6
Alignment explanation
Indices: 22673289--22673319 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
22673279 TCATTCTTTC
22673289 CCATTT CCATTT CCATTT CCATTT CCATTT C
1 CCATTT CCATTT CCATTT CCATTT CCATTT C
22673320 GAAGATCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.48
Consensus pattern (6 bp):
CCATTT
Found at i:22678391 original size:25 final size:25
Alignment explanation
Indices: 22678360--22678478 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
22678350 GCTCTCTCTT
*
22678360 GAGCCATATAACAGGAAGCTCATAT
1 GAGCCATATAACAGGAAGCTCATAC
* * *
22678385 GAGCCATGTAACAGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATAC
* ** *
22678410 GGGCTGTATAACGGGAAGCTCAT-C
1 GAGCCATATAACAGGAAGCTCATAC
* *
22678434 AGAGCCATA-ATCAGGAAGCTCATGC
1 -GAGCCATATAACAGGAAGCTCATAC
*
22678459 GAGCCA-ATAACAGGTAGCTC
1 GAGCCATATAACAGGAAGCTC
22678479 CGGATAGCCA
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 29 0.39
25 44 0.59
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAC
Found at i:22678488 original size:48 final size:47
Alignment explanation
Indices: 22678434--22678552 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 47
22678424 GAAGCTCATC
* * *
22678434 AGAGCCATAATCAGGAAGCTCATGCGAGCCAATAACAGGTAGCTCCGG
1 AGAGCCATAATCAGGAAGCTCAAGCGAGCC-ATAACAGGAAGCTCCGA
* * * * *
22678482 ATAGCCATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGA
1 AGAGCCATA-ATCAGGAAGCTCAAGCGAGCCATAACAGGAAGCTCCGA
*
22678530 AGAGCCATTAATCAGTAAGCTCA
1 AGAGCCA-TAATCAGGAAGCTCA
22678553 GAAAGAGCCT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
48 37 0.65
49 20 0.35
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.18
Consensus pattern (47 bp):
AGAGCCATAATCAGGAAGCTCAAGCGAGCCATAACAGGAAGCTCCGA
Found at i:22678595 original size:26 final size:26
Alignment explanation
Indices: 22678484--22678604 Score: 92
Period size: 26 Copynumber: 4.8 Consensus size: 26
22678474 AGCTCCGGAT
* **
22678484 AGCCATATATCGGGAAGTTCA-AGCG
1 AGCCATATATCGGGAAGCTCACAAAG
*
22678509 AGCC--ATATCGGGAAGCTC-CGAAG
1 AGCCATATATCGGGAAGCTCACAAAG
* * *
22678532 AGCCAT-TAATCAGTAAGCTCAGAAAG
1 AGCCATAT-ATCGGGAAGCTCACAAAG
* *
22678558 AGCC-TTTAATCGAGAAGCTCACAAAG
1 AGCCATAT-ATCGGGAAGCTCACAAAG
*
22678584 AGCCATATATCGGGACGCTCA
1 AGCCATATATCGGGAAGCTCA
22678605 TAAGAGTTGC
Statistics
Matches: 74, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
23 18 0.24
24 1 0.01
25 15 0.20
26 38 0.51
27 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
AGCCATATATCGGGAAGCTCACAAAG
Found at i:22686660 original size:27 final size:28
Alignment explanation
Indices: 22686606--22686670 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 28
22686596 ATAAAAAATA
22686606 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
22686634 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
22686661 ACCAAAATAT
1 ACCAAAATAT
22686671 ACCAAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:22686753 original size:27 final size:27
Alignment explanation
Indices: 22686723--22686774 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
22686713 CACCCTGGTC
* *
22686723 GTGCCAAGGTGATTGGCAGCACCAAAG
1 GTGCCAAAGTCATTGGCAGCACCAAAG
**
22686750 GTGCCAAAGTCATTGGTGGCACCAA
1 GTGCCAAAGTCATTGGCAGCACCAA
22686775 TGTTATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (27 bp):
GTGCCAAAGTCATTGGCAGCACCAAAG
Found at i:22686824 original size:4 final size:4
Alignment explanation
Indices: 22686815--22686931 Score: 61
Period size: 4 Copynumber: 29.0 Consensus size: 4
22686805 GAATGAGAGG
* * *
22686815 GAAA GAAA GAAA GAAA GGAAT GAGAG GAAA GAAA GAAAA GGAAA G-GA
1 GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA G-AAA -GAAA GAAA
22686862 GAAGA GAAA -AAA -AAA GAAA G-AA G-AA GAAGA TGAAA GGAGAA GAAA
1 GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA -GA-AA GAAA
*
22686907 -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
22686932 AGGAAAGGAG
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
3 21 0.23
4 42 0.46
5 22 0.24
6 6 0.07
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:22686835 original size:27 final size:28
Alignment explanation
Indices: 22686805--22686861 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
22686795 GTGGGGGGGA
22686805 GAATGAGAGGGAAAGAAAG-AAA-GAAAG
1 GAATGAGA-GGAAAGAAAGAAAAGGAAAG
22686832 GAATGAGAGGAAAGAAAGAAAAGGAAAG
1 GAATGAGAGGAAAGAAAGAAAAGGAAAG
22686860 GA
1 GA
22686862 GAAGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 10 0.36
27 11 0.39
28 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (28 bp):
GAATGAGAGGAAAGAAAGAAAAGGAAAG
Found at i:22686849 original size:26 final size:26
Alignment explanation
Indices: 22686805--22686931 Score: 89
Period size: 28 Copynumber: 4.7 Consensus size: 26
22686795 GTGGGGGGGA
22686805 GAATGAGAGGGAAAGAAAGAAAGAAAG
1 GAATGAGA-GGAAAGAAAGAAAGAAAG
22686832 GAATGAGAGGAAAGAAAGAAAAGGAAAG
1 GAATGAGAGGAAAGAAAG-AAA-GAAAG
* * *
22686860 GAGAAGAGA-AAAAAAAAGAAAGAAGAAG
1 GA-ATGAGAGGAAAGAAAGAAAG-A-AAG
* *
22686888 AAGATGAAAGGAGAAGAAA-AAAGAAA-
1 GA-ATGAGAGGA-AAGAAAGAAAGAAAG
**
22686914 GAAAAAGAAGGAAAGAAA
1 GAATGAG-AGGAAAGAAA
22686932 AGGAAAGGAG
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
25 8 0.10
26 16 0.20
27 17 0.21
28 24 0.30
29 10 0.12
30 5 0.06
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.02
Consensus pattern (26 bp):
GAATGAGAGGAAAGAAAGAAAGAAAG
Found at i:22686869 original size:22 final size:21
Alignment explanation
Indices: 22686818--22686949 Score: 84
Period size: 22 Copynumber: 6.4 Consensus size: 21
22686808 TGAGAGGGAA
*
22686818 AGAAAGAAAG-AAAGGAATGAG
1 AGAAAGAAAGAAAAGGAAAG-G
22686839 AGGAAAGAAAGAAAAGGAAAGG
1 A-GAAAGAAAGAAAAGGAAAGG
* * *
22686861 AGAAGAGAAAAAAAAAGAAAGA
1 AGAA-AGAAAGAAAAGGAAAGG
*
22686883 AG-AAG-AAGATGAAAGG--AGA
1 AGAAAGAAAGA--AAAGGAAAGG
*
22686902 AGAAA-AAAG-AAA-GAAA-A
1 AGAAAGAAAGAAAAGGAAAGG
*
22686919 AGAAGGAAAGAAAAGGAAAGG
1 AGAAAGAAAGAAAAGGAAAGG
22686940 AGAAGAGAAA
1 AGAA-AGAAA
22686950 TGATTAAATG
Statistics
Matches: 88, Mismatches: 9, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
16 1 0.01
17 8 0.09
18 5 0.06
19 11 0.12
20 11 0.12
21 13 0.15
22 31 0.35
23 8 0.09
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAGAAAAGGAAAGG
Found at i:22686881 original size:36 final size:36
Alignment explanation
Indices: 22686841--22686949 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 36
22686831 GGAATGAGAG
22686841 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
*
22686877 GAAAG-AAGAAGAAGATGAAAGGAGAAGAAAAAAGAAAGAAAAA
1 GAAAGAAAGAA-AAG--GAAAGGAGAAG-----AGAAAAAAAAA
*
22686920 GAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAA
22686950 TGATTAAATG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
35 5 0.08
36 13 0.21
38 11 0.18
41 11 0.18
43 17 0.27
44 5 0.08
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (36 bp):
GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
Found at i:22686888 original size:10 final size:10
Alignment explanation
Indices: 22686843--22686945 Score: 58
Period size: 10 Copynumber: 10.4 Consensus size: 10
22686833 AATGAGAGGA
22686843 AAGAAAGAA-
1 AAGAAAGAAG
*
22686852 AAGGAAAGGAG
1 AA-GAAAGAAG
22686863 AAGAGAA-AA-
1 AAGA-AAGAAG
22686872 AA-AAAGAAAG
1 AAGAAAG-AAG
22686882 AAG-AAGAAG
1 AAGAAAGAAG
* *
22686891 ATGAAAGGAG
1 AAGAAAGAAG
*
22686901 AAGAAAAAAG
1 AAGAAAGAAG
22686911 AAAGAAA-AAG
1 -AAGAAAGAAG
22686921 AAGGAAAGAA-
1 AA-GAAAGAAG
*
22686931 AAGGAAAGGAG
1 AA-GAAAGAAG
22686942 AAGA
1 AAGA
22686946 GAAATGATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 13 0.18
10 44 0.59
11 14 0.19
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:22686899 original size:43 final size:41
Alignment explanation
Indices: 22686845--22686949 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 41
22686835 TGAGAGGAAA
22686845 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG--AAAGAA-
1 GAAA-AAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
* * * *
22686884 GAAGAAGATGAAAGGAGAAGA-AAAAAGAAAGAAAAAGAAG
1 GAAAAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
22686924 GAAAGAAAAGGAAAGGAGAAGAGAAA
1 GAAA-AAAAGGAAAGGAGAAGAGAAA
22686950 TGATTAAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
37 9 0.17
38 15 0.28
39 9 0.17
40 3 0.06
41 15 0.28
42 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (41 bp):
GAAAAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
Found at i:22689683 original size:3 final size:3
Alignment explanation
Indices: 22689675--22689700 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22689665 TCTTAATACT
22689675 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
22689701 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:22689705 original size:3 final size:3
Alignment explanation
Indices: 22689699--22689784 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
22689689 CAACAACAAC
22689699 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
22689747 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22689785 CTAAAACTAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22689971 original size:12 final size:12
Alignment explanation
Indices: 22689954--22689978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22689944 CCTCTTCTTG
22689954 TTCTTATTTTTC
1 TTCTTATTTTTC
22689966 TTCTTATTTTTC
1 TTCTTATTTTTC
22689978 T
1 T
22689979 CCCTTCAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTATTTTTC
Found at i:22690064 original size:27 final size:27
Alignment explanation
Indices: 22690018--22690119 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 27
22690008 AACACGAGTA
*
22690018 GTGCCGCCAATCA-GTATGGCACTATTG
1 GTGCCGCCAATCACCT-TGGCACTATTG
* * * *
22690045 GTGCCGCCAGTCTCCTTGGCACCATCG
1 GTGCCGCCAATCACCTTGGCACTATTG
*
22690072 GTGCCGCCAATCACTTTGGCACCT-TTG
1 GTGCCGCCAATCACCTTGGCA-CTATTG
*
22690099 GTGCCGCCAATCATCTTGGCA
1 GTGCCGCCAATCACCTTGGCA
22690120 TGACCAGGGT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 59 0.97
28 2 0.03
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAATCACCTTGGCACTATTG
Found at i:22690209 original size:26 final size:27
Alignment explanation
Indices: 22690180--22690242 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
22690170 GTTTTTTGGT
22690180 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
*
22690206 ATATTTGGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
22690233 ATATTTTGGT
1 ATATTTTGGT
22690243 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:22693815 original size:44 final size:44
Alignment explanation
Indices: 22693765--22693854 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
22693755 TGATAGTTAA
22693765 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
1 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
22693809 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
1 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
22693853 AT
1 AT
22693855 TAACCCATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (44 bp):
ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
Found at i:22696432 original size:26 final size:26
Alignment explanation
Indices: 22696382--22696429 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 26
22696372 TAATGAAAGG
22696382 AAAAGAAAAAAAGAAGAATAAAACAT
1 AAAAGAAAAAAAGAAGAATAAAACAT
22696408 AAAAG---AAAAGAAGAATAAAACA
1 AAAAGAAAAAAAGAAGAATAAAACA
22696430 ACAACAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 17 0.77
26 5 0.23
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAGAATAAAACAT
Found at i:22701455 original size:4 final size:4
Alignment explanation
Indices: 22701446--22701470 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22701436 TAATGGACAT
22701446 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
22701471 CATCAAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:22703511 original size:16 final size:16
Alignment explanation
Indices: 22703490--22703520 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22703480 CACCTAAGAC
22703490 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
*
22703506 ACACCTCAATCTTAT
1 ACACCTCAACCTTAT
22703521 CTGGATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:22704126 original size:21 final size:21
Alignment explanation
Indices: 22704100--22704149 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
22704090 GTTTCCACAT
22704100 GCCCATGTCACTTACCCAGAC
1 GCCCATGTCACTTACCCAGAC
22704121 GCCCATGTCACTTACCCAGAC
1 GCCCATGTCACTTACCCAGAC
22704142 GCCCATGT
1 GCCCATGT
22704150 GCAACCCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (21 bp):
GCCCATGTCACTTACCCAGAC
Found at i:22705159 original size:41 final size:41
Alignment explanation
Indices: 22705102--22705184 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
22705092 ATAGTGCCTC
22705102 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
1 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
22705143 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
1 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
22705184 A
1 A
22705185 TCTACTCCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (41 bp):
AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
Found at i:22705461 original size:21 final size:21
Alignment explanation
Indices: 22705422--22705477 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
22705412 AAATCAAGCA
*
22705422 ATTCATTTACCAA-TTCCCAT
1 ATTCAATTACCAATTTCCCAT
22705442 ATTCAATTACCAATTTCCCAT
1 ATTCAATTACCAATTTCCCAT
22705463 ATTCAATTACCAATT
1 ATTCAATTACCAATT
22705478 GTAACACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 12 0.35
21 22 0.65
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTCAATTACCAATTTCCCAT
Found at i:22705617 original size:20 final size:20
Alignment explanation
Indices: 22705592--22705631 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22705582 CGTAAAATGA
*
22705592 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
22705612 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
22705632 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:22705621 original size:34 final size:35
Alignment explanation
Indices: 22705577--22705643 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
22705567 CAGTAAAATA
*
22705577 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
22705611 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
22705644 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:22705647 original size:14 final size:15
Alignment explanation
Indices: 22705571--22705647 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
22705561 GATTGCCAGT
* *
22705571 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
22705585 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
22705599 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
22705619 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
22705634 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
22705648 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:22707002 original size:12 final size:12
Alignment explanation
Indices: 22706985--22707009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22706975 CTTTGATTCG
22706985 TTCTAAATCATT
1 TTCTAAATCATT
22706997 TTCTAAATCATT
1 TTCTAAATCATT
22707009 T
1 T
22707010 GATTGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCTAAATCATT
Found at i:22707491 original size:17 final size:21
Alignment explanation
Indices: 22707451--22707496 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
22707441 ATTATTTTAA
22707451 AATTATTTTTCGATCTAAATT
1 AATTATTTTTCGATCTAAATT
22707472 AATTATTTTTC-A-CT-AA-T
1 AATTATTTTTCGATCTAAATT
22707489 AATTATTT
1 AATTATTT
22707497 AATTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 2 0.08
20 1 0.04
21 11 0.44
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTATTTTTCGATCTAAATT
Found at i:22711971 original size:138 final size:139
Alignment explanation
Indices: 22711723--22711997 Score: 419
Period size: 138 Copynumber: 2.0 Consensus size: 139
22711713 GGAGAACAAT
* * * * * *
22711723 AGGCTATAAGTGGATTTTTAAGCTACAAAAGAATGGTGATGGGACTATACCCAGATATAAGGCCA
1 AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
*
22711788 AACTAGTGGTCAAAGGGTATCTCCAAGAAATTGGTATTGATTTCCAAGAAACTTTTAG-CCTCTG
66 AACTAGTGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCTG
22711852 GTCAAACGA
131 GTCAAACGA
* * * *
22711861 AGGCTAGAAGTGGATTTTTAATCTAAAAAAGAATGATGATGGAAATATAGCTATATACAAGGCCA
1 AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
*
22711926 AACT-GATGGTCAAAGGGTATCTCCAAGAAGCTGGTATTGATTTCCAAGAAACTTTTAGTCCTCT
66 AACTAG-TGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCT
22711990 GGTCAAAC
130 GGTCAAAC
22711998 CAGCTACTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
137 1 0.01
138 109 0.89
139 13 0.11
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (139 bp):
AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
AACTAGTGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCTG
GTCAAACGA
Found at i:22713252 original size:55 final size:55
Alignment explanation
Indices: 22713168--22713276 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
22713158 ACCAAACCTC
*
22713168 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACTTTGGTGTTGTTAGCAAGTA
1 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGTA
22713223 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGT
1 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGT
22713277 CACTAGGAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (55 bp):
TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGTA
Found at i:22714114 original size:13 final size:13
Alignment explanation
Indices: 22714098--22714129 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
22714088 TTTAAACCAA
22714098 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
*
22714111 ACTTCTCAAAAAC
1 ACTTTTCAAAAAC
22714124 ACTTTT
1 ACTTTT
22714130 TCACTGCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:22715491 original size:20 final size:20
Alignment explanation
Indices: 22715466--22715512 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
22715456 GATTGAGTTT
*
22715466 TTTTTTTTCTCAAAAGAGTA
1 TTTTTTTTCTCAAAAGAGAA
22715486 TTTTTTTTCTCAAAAGAGAA
1 TTTTTTTTCTCAAAAGAGAA
22715506 TTTTTTT
1 TTTTTTT
22715513 CTGGTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTTTTTCTCAAAAGAGAA
Found at i:22720475 original size:45 final size:45
Alignment explanation
Indices: 22720411--22720501 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
22720401 CTATCTCGAG
22720411 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
1 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
*
22720456 TTTCCAAGATATTTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
1 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
22720501 T
1 T
22720502 AATTGTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (45 bp):
TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
Found at i:22732239 original size:17 final size:19
Alignment explanation
Indices: 22732217--22732266 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
22732207 AGATTACTAT
*
22732217 ATAAAAAA-ATTTAA-TAA
1 ATAAAAAATATTAAATTAA
22732234 ATAAAAAATATTAAATTAA
1 ATAAAAAATATTAAATTAA
22732253 ATAATATAAATATT
1 ATAA-A-AAATATT
22732267 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.29
18 5 0.18
19 7 0.25
20 1 0.04
21 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATATTAAATTAA
Found at i:22732684 original size:9 final size:9
Alignment explanation
Indices: 22732670--22732700 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22732660 TTTGGTTAAA
22732670 AATTAACCG
1 AATTAACCG
22732679 AATTAACCG
1 AATTAACCG
*
22732688 AATTAACTG
1 AATTAACCG
22732697 AATT
1 AATT
22732701 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:22735310 original size:16 final size:17
Alignment explanation
Indices: 22735285--22735318 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22735275 ATCATTTTCT
*
22735285 TTTAATTATAT-AATTA
1 TTTAAATATATCAATTA
22735301 TTTAAATATATCAATTA
1 TTTAAATATATCAATTA
22735318 T
1 T
22735319 AAATTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATATATCAATTA
Found at i:22737193 original size:2 final size:2
Alignment explanation
Indices: 22737186--22737217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22737176 ATGTGAATTG
22737186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22737218 GTAAACATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22760833 original size:17 final size:17
Alignment explanation
Indices: 22760811--22760843 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22760801 TTATTCTATT
22760811 TAATTA-ATTTTACTAAA
1 TAATTATATTTT-CTAAA
22760828 TAATTATATTTTCTAA
1 TAATTATATTTTCTAA
22760844 TGTTGCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTTTCTAAA
Found at i:22767095 original size:15 final size:17
Alignment explanation
Indices: 22767065--22767096 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
22767055 AAATATTTAT
22767065 ACAATTATTATATAATA
1 ACAATTATTATATAATA
22767082 ACAA-TATT-TATAATA
1 ACAATTATTATATAATA
22767097 TATTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ACAATTATTATATAATA
Found at i:22771228 original size:2 final size:2
Alignment explanation
Indices: 22771221--22771271 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
22771211 AGCAGAAAGC
22771221 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
22771263 CT CT CT CT C
1 CT CT CT CT C
22771272 ACAGTTTCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:22772833 original size:20 final size:20
Alignment explanation
Indices: 22772805--22772906 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
22772795 AGATGTTAAT
*
22772805 ATTTCTAATGCAAAACCAAA
1 ATTTCTAATGCAAAACAAAA
* *
22772825 ATTTGTAAT-CAATACAAAA
1 ATTTCTAATGCAAAACAAAA
*
22772844 ATTTCTAATGCAATATC-AAA
1 ATTTCTAATGCAA-AACAAAA
* * * *
22772864 ATATC-AATGCTATATAAAA
1 ATTTCTAATGCAAAACAAAA
* * *
22772883 ATCTCTAATGCAATACCAAA
1 ATTTCTAATGCAAAACAAAA
22772903 ATTT
1 ATTT
22772907 TTAAGAATAT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
19 29 0.47
20 32 0.52
21 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTCTAATGCAAAACAAAA
Found at i:22772846 original size:19 final size:21
Alignment explanation
Indices: 22772805--22772903 Score: 93
Period size: 19 Copynumber: 5.0 Consensus size: 21
22772795 AGATGTTAAT
* *
22772805 ATTTCTAATGCAA-AACCAAA
1 ATTTCTAATGCAATATCAAAA
*
22772825 ATTTGTAAT-CAATA-CAAAA
1 ATTTCTAATGCAATATCAAAA
22772844 ATTTCTAATGCAATATC-AAA
1 ATTTCTAATGCAATATCAAAA
* *
22772864 ATATC-AATGCTATAT-AAAA
1 ATTTCTAATGCAATATCAAAA
* *
22772883 ATCTCTAATGCAATACCAAAA
1 ATTTCTAATGCAATATCAAAA
22772904 TTTTTAAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 31 0.48
20 29 0.45
21 5 0.08
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.29
Consensus pattern (21 bp):
ATTTCTAATGCAATATCAAAA
Found at i:22772848 original size:39 final size:39
Alignment explanation
Indices: 22772805--22772906 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
22772795 AGATGTTAAT
* *
22772805 ATTTCTAATGCAAAACCAAAATTTGTAAT-CAATACAAAA
1 ATTTCTAATGCAATACCAAAATTT-CAATGCAATACAAAA
* * * *
22772844 ATTTCTAATGCAATATCAAAATATCAATGCTATATAAAA
1 ATTTCTAATGCAATACCAAAATTTCAATGCAATACAAAA
*
22772883 ATCTCTAATGCAATACCAAAATTT
1 ATTTCTAATGCAATACCAAAATTT
22772907 TTAAGAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 3 0.06
39 50 0.94
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (39 bp):
ATTTCTAATGCAATACCAAAATTTCAATGCAATACAAAA
Found at i:22775094 original size:21 final size:21
Alignment explanation
Indices: 22775070--22775144 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 21
22775060 AAAGAAATTG
22775070 AAAAATCATTTTAAAAAATTC-
1 AAAAAT-ATTTTAAAAAATTCT
*
22775091 -AAAATATTTATAAAAAAATCT
1 AAAAATATTT-TAAAAAATTCT
22775112 AAAATTTATATTTTTAAAAAATTCT
1 AAAA---ATA-TTTTAAAAAATTCT
22775137 AAAAATAT
1 AAAAATAT
22775145 ATAAAGAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.09
20 14 0.31
21 1 0.02
22 6 0.13
25 17 0.38
26 3 0.07
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATATTTTAAAAAATTCT
Found at i:22775118 original size:19 final size:20
Alignment explanation
Indices: 22775071--22775121 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
22775061 AAGAAATTGA
*
22775071 AAAATCATTT-TAAAAAATTC
1 AAAAT-ATTTATAAAAAAATC
22775091 AAAATATTTATAAAAAAATC
1 AAAATATTTATAAAAAAATC
*
22775111 TAAA-ATTTATA
1 AAAATATTTATA
22775122 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATTTATAAAAAAATC
Found at i:22786500 original size:25 final size:23
Alignment explanation
Indices: 22786472--22786542 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
22786462 CCAATATATA
22786472 GCTCTTCGAAGCTTCCCGATAACTG
1 GCTCTTCG-AGCTTCCCGATAA-TG
* *
22786497 GCTCTTATGGGCTTCCCGATTAATG
1 GCTCTT-CGAGCTTCCCGA-TAATG
* *
22786522 GCTCTCCGGAGCTTCCAGATA
1 GCTCTTC-GAGCTTCCCGATA
22786543 TTGACTCCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.05
25 31 0.84
26 4 0.11
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.30
Consensus pattern (23 bp):
GCTCTTCGAGCTTCCCGATAATG
Found at i:22788558 original size:2 final size:2
Alignment explanation
Indices: 22788551--22788583 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22788541 CATCCATCAC
22788551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22788584 CTACTACTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22790724 original size:14 final size:15
Alignment explanation
Indices: 22790707--22790739 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
22790697 TCTTTCCATT
22790707 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
22790721 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
22790736 -CTTT
1 TCTTT
22790740 ATTATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:22793682 original size:45 final size:45
Alignment explanation
Indices: 22793632--22793722 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
22793622 GAAGGAAACT
*
22793632 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTGGGTAATTA
1 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
22793677 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
1 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
22793722 A
1 A
22793723 TCCTTCTAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (45 bp):
AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
Found at i:22805804 original size:21 final size:21
Alignment explanation
Indices: 22805778--22805820 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22805768 TGATGCCAAG
*
22805778 TCCATCTACTTAGATTTTCCC
1 TCCATCTACTTAGAATTTCCC
22805799 TCCATCTACTTAGAATTTCCC
1 TCCATCTACTTAGAATTTCCC
22805820 T
1 T
22805821 TACTACACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.42
Consensus pattern (21 bp):
TCCATCTACTTAGAATTTCCC
Found at i:22813575 original size:12 final size:12
Alignment explanation
Indices: 22813558--22813583 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22813548 TTAGGTTTCC
22813558 AAAAATGGAAAT
1 AAAAATGGAAAT
22813570 AAAAATGGAAAT
1 AAAAATGGAAAT
22813582 AA
1 AA
22813584 TCCATTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAAATGGAAAT
Found at i:22814229 original size:30 final size:30
Alignment explanation
Indices: 22814193--22814261 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
22814183 TATTTCTATT
*
22814193 AAGAAGAGAGAATTTTCATTTTCACCCTAA
1 AAGAAGAGAGAATTTTCATTTTCACCCCAA
**
22814223 AAGAAGAGAGAATTTTTGTTTTCACCCCAA
1 AAGAAGAGAGAATTTTCATTTTCACCCCAA
*
22814253 AAGGAGAGA
1 AAGAAGAGA
22814262 AAACTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (30 bp):
AAGAAGAGAGAATTTTCATTTTCACCCCAA
Found at i:22820341 original size:26 final size:26
Alignment explanation
Indices: 22820311--22820373 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
22820301 ATGAAATTTC
*
22820311 TCAAAATTTTACCAAGGGTAAAATCA
1 TCAAAATTTTAACAAGGGTAAAATCA
* ** **
22820337 TCAAATTTTTAACGGGGGTAAAATTG
1 TCAAAATTTTAACAAGGGTAAAATCA
22820363 TCAAAATTTTA
1 TCAAAATTTTA
22820374 TTAGAGGTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTAACAAGGGTAAAATCA
Found at i:22834187 original size:29 final size:30
Alignment explanation
Indices: 22834137--22834197 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
22834127 AAGTTTTCGT
*
22834137 TTTGGTCACTTAACTAAACAAA-TTTACAA
1 TTTGGTCACTAAACTAAACAAAGTTTACAA
** *
22834166 TTTGGTCACTAAACTATTCAAAGTTTTCAA
1 TTTGGTCACTAAACTAAACAAAGTTTACAA
22834196 TT
1 TT
22834198 AAGCCGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTGGTCACTAAACTAAACAAAGTTTACAA
Found at i:22834671 original size:14 final size:14
Alignment explanation
Indices: 22834648--22834679 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
22834638 GACGATTCTC
*
22834648 AAAAGTAAAAGAAA
1 AAAAGAAAAAGAAA
22834662 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
22834676 AAAA
1 AAAA
22834680 AAATTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:22854492 original size:19 final size:19
Alignment explanation
Indices: 22854449--22854485 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22854439 AATTGAGGAT
22854449 TAGAAACGAGATTAGAATG
1 TAGAAACGAGATTAGAATG
*
22854468 TAGAAATGAGATTAGAAT
1 TAGAAACGAGATTAGAAT
22854486 TTTGAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (19 bp):
TAGAAACGAGATTAGAATG
Found at i:22856733 original size:6 final size:6
Alignment explanation
Indices: 22856725--22856754 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22856715 GTAGACGTGT
*
22856725 GAATGT GAATGC GAATGC GAATGC GAATGC
1 GAATGC GAATGC GAATGC GAATGC GAATGC
22856755 TCAAGGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (6 bp):
GAATGC
Found at i:22885486 original size:28 final size:30
Alignment explanation
Indices: 22885432--22885487 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
22885422 ATTTTTCCAT
* *
22885432 TGATGAATCTATGTGATTTTAGATGTTAAA
1 TGATGAATCTATGAGATATTAGATGTTAAA
*
22885462 TGATGAAT-T-TGAGATATTAGTTGTTA
1 TGATGAATCTATGAGATATTAGATGTTA
22885488 TTTAAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 1 0.04
30 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (30 bp):
TGATGAATCTATGAGATATTAGATGTTAAA
Found at i:22886176 original size:75 final size:74
Alignment explanation
Indices: 22885991--22886210 Score: 224
Period size: 75 Copynumber: 2.9 Consensus size: 74
22885981 ATGCAGTGAT
* * * *
22885991 TTTGGGCTATGTGCCTTGTAGGCTTTGTACCGGTGATTTTGGGATATGTGCCTAGCAGGCTTTGT
1 TTTGGGCTATGTGCCTAG-AAGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
**
22886056 GCCGATGTTA
65 GCCGATCATA
* * * * *
22886066 TTTGGGCTATGTGCTTAGTAGAATTTGTGCTGGTGATTTTGGGCTATGTGCCTAGCAGGGTTTGT
1 TTTGGGCTATGTGCCTAGAAG-CTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
** *
22886131 GTTGGTCATA
65 GCCGATCATA
* * * * * *
22886141 TTTGGGCTTTGTGCCTAGCAAGCTTTATGCCGGTGATATTCGAGCTCTGTGCCTAGTAGGCTTTG
1 TTTGGGCTATGTGCCTAG-AAGCTTTGTGCCGGTGAT-TTTGGGCTATGTGCCTAGCAGGCTTTG
22886206 TGCCG
64 TGCCG
22886211 GTGATATTCG
Statistics
Matches: 115, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
74 1 0.01
75 87 0.76
76 27 0.23
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.39
Consensus pattern (74 bp):
TTTGGGCTATGTGCCTAGAAGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGTG
CCGATCATA
Found at i:22886226 original size:38 final size:38
Alignment explanation
Indices: 22885986--22886218 Score: 247
Period size: 38 Copynumber: 6.2 Consensus size: 38
22885976 TAGAAATGCA
* * *
22885986 GTGAT-TTTGGGCTATGTGCCTTGTAGGCTTTGTACCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
*
22886023 GTGAT-TTTGGGATATGTGCCTAGCAGGCTTTGTGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * * ** *
22886060 ATGTTATTTGGGCTATGTGCTTAGTAGAATTTGTGCTG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* **
22886098 GTGAT-TTTGGGCTATGTGCCTAGCAGGGTTTGTGTTG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * *
22886135 GTCATATTTGGGCTTTGTGCCTAGCAAGCTTTATGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * *
22886173 GTGATATTCGAGCTCTGTGCCTAGTAGGCTTTGTGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
22886211 GTGATATT
1 GTGATATT
22886219 CGAGCTCTAT
Statistics
Matches: 161, Mismatches: 33, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
37 67 0.42
38 94 0.58
ACGTcount: A:0.14, C:0.15, G:0.32, T:0.39
Consensus pattern (38 bp):
GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
Found at i:22886243 original size:38 final size:38
Alignment explanation
Indices: 22886152--22886246 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
22886142 TTGGGCTTTG
* *
22886152 TGCCTAGCAAGCTTTATGCCGGTGATATTCGAGCTCTG
1 TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
* *
22886190 TGCCTAGTAGGCTTTGTGCCGGTGATATTCGAGCTCTA
1 TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
* *
22886228 TGGCTAGCAACCTTTGTGC
1 TGCCTAGCAAGCTTTGTGC
22886247 AAGTGTATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (38 bp):
TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
Found at i:22886329 original size:41 final size:41
Alignment explanation
Indices: 22886249--22886345 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
22886239 CTTTGTGCAA
* * * *
22886249 GTGTATTATATCAGGCTTTGTGCTTAGTTGGCTTTGTGCCG
1 GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
* * * *
22886290 GTGTGTTATATCAGGCTTCGAGCTTGGTAGTCTTCGTGCCA
1 GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
* *
22886331 ATGTATTGTATCAGG
1 GTGTATTATATCAGG
22886346 TAAGTTGTAC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
Found at i:22893696 original size:41 final size:41
Alignment explanation
Indices: 22893616--22893738 Score: 117
Period size: 41 Copynumber: 3.0 Consensus size: 41
22893606 GATATTAAAC
* * * *
22893616 CAAGCTCTATGCCTAGCAGGCTTTGTGCTTG-TGACTTATAT
1 CAAGCTCTGTGCCTAGCAGGCTTCGTGC-CGATGATTTATAT
*
22893657 CAAGCTCTGTGCCTAGCAGGCTTCATGCCGATGATTTATAT
1 CAAGCTCTGTGCCTAGCAGGCTTCGTGCCGATGATTTATAT
* * * *
22893698 CAGGCT-TAGTACCTAACAGGCTTCGTTCC-AGTGATTTATAT
1 CAAGCTCT-GTGCCTAGCAGGCTTCGTGCCGA-TGATTTATAT
22893739 TAGAATTTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
41 66 0.96
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (41 bp):
CAAGCTCTGTGCCTAGCAGGCTTCGTGCCGATGATTTATAT
Found at i:22899592 original size:41 final size:41
Alignment explanation
Indices: 22899526--22899620 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
22899516 GAGATAATAA
* * * **
22899526 ATCAAGCTCTGTACCTAGTAGGCTTCGTGCCGGTGATTTAT
1 ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
*
22899567 ATCAGGCTCTGTGCCTAGCAAGCTTCGTGCCAATGATTTAT
1 ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
*
22899608 ATCAGGCTTTGTA
1 ATCAGGCTCTGTA
22899621 GAAAGCTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (41 bp):
ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
Found at i:22899641 original size:37 final size:40
Alignment explanation
Indices: 22899547--22899646 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 40
22899537 TACCTAGTAG
* *
22899547 GCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCTAGCAA
1 GCTTCGTGCCAGTGATTTATATCAGGCTCTGTG-CTAGAAA
*
22899588 GCTTCGTGCCAATGATTTATATCAGGCT-T-TG-TAGAAA
1 GCTTCGTGCCAGTGATTTATATCAGGCTCTGTGCTAGAAA
* *
22899625 GCTTGGTGTCAGTGATTTATAT
1 GCTTCGTGCCAGTGATTTATAT
22899647 TAGCAAGCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 24 0.45
39 2 0.04
40 1 0.02
41 26 0.49
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
GCTTCGTGCCAGTGATTTATATCAGGCTCTGTGCTAGAAA
Found at i:22904512 original size:21 final size:22
Alignment explanation
Indices: 22904483--22904540 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
22904473 TGTAGGGGTA
* *
22904483 CACACGCCCATGTGAA-GGAGG
1 CACATGCCCGTGTGAAGGGAGG
*
22904504 CACATGCCCGGGTGAAGGGAGG
1 CACATGCCCGTGTGAAGGGAGG
*
22904526 CACATGGCCGTGTGA
1 CACATGCCCGTGTGA
22904541 CTATGACACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.24, C:0.26, G:0.38, T:0.12
Consensus pattern (22 bp):
CACATGCCCGTGTGAAGGGAGG
Found at i:22906597 original size:12 final size:12
Alignment explanation
Indices: 22906569--22906604 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
22906559 GCAAATGAAT
*
22906569 CATTTCTCATTTT
1 CATTTC-CATTTC
22906582 CATTTCCATTTC
1 CATTTCCATTTC
22906594 CATTTCCATTT
1 CATTTCCATTT
22906605 TGAGAAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTCCATTTC
Found at i:22906603 original size:18 final size:19
Alignment explanation
Indices: 22906569--22906604 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22906559 GCAAATGAAT
*
22906569 CATTTCTCATTTTCATTTC
1 CATTTCTCATTTCCATTTC
22906588 CATTTC-CATTTCCATTT
1 CATTTCTCATTTCCATTT
22906605 TGAGAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (19 bp):
CATTTCTCATTTCCATTTC
Found at i:22908705 original size:20 final size:21
Alignment explanation
Indices: 22908680--22908725 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
22908670 ATTGAATTTA
22908680 TTTTATCTTTT-TTTATAT-AT
1 TTTTAT-TTTTATTTATATGAT
*
22908700 TTTTATTTTTATTTGTATGAT
1 TTTTATTTTTATTTATATGAT
22908721 TTTTA
1 TTTTA
22908726 ATAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATTTTTATTTATATGAT
Found at i:22909043 original size:29 final size:29
Alignment explanation
Indices: 22909010--22909100 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
22909000 GAAACTGTTG
*
22909010 AATTATCTTTTCTTTATCAATGTTGTTAA
1 AATTATCTTCTCTTTATCAATGTTGTTAA
* *
22909039 AATTAT-TATGTGTTTGA--AACTGTTG----
1 AATTATCT-TCTCTTT-ATCAA-TGTTGTTAA
22909064 AATTATCTTCTCTTTATCAATGTTGTTAA
1 AATTATCTTCTCTTTATCAATGTTGTTAA
22909093 AATTATCT
1 AATTATCT
22909101 CCTTATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 20
0.67 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 16 0.33
26 3 0.06
28 3 0.06
29 24 0.50
30 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
AATTATCTTCTCTTTATCAATGTTGTTAA
Found at i:22909056 original size:54 final size:54
Alignment explanation
Indices: 22908992--22909098 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
22908982 ACACTTTCTC
*
22908992 ATGTGTTTGAAACTGTTGAATTATCTTTTCTTTATCAATGTTGTTAAAATTATT
1 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTATT
22909046 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTAT
1 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTAT
22909099 CTCCTTATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (54 bp):
ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTATT
Found at i:22915508 original size:25 final size:25
Alignment explanation
Indices: 22915480--22915532 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
22915470 CTCAACTAAA
22915480 TAATCCAACTCGAAATATAAAATTT
1 TAATCCAACTCGAAATATAAAATTT
22915505 TAATCCAACTCGAAATATAAAATTT
1 TAATCCAACTCGAAATATAAAATTT
22915530 TAA
1 TAA
22915533 AAATTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (25 bp):
TAATCCAACTCGAAATATAAAATTT
Found at i:22923132 original size:15 final size:15
Alignment explanation
Indices: 22923112--22923146 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
22923102 CTTTCAAAGT
22923112 ACATATCAATTTCAC
1 ACATATCAATTTCAC
22923127 ACATATCAATTTCAC
1 ACATATCAATTTCAC
22923142 ACATA
1 ACATA
22923147 CTTGAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (15 bp):
ACATATCAATTTCAC
Found at i:22930354 original size:5 final size:5
Alignment explanation
Indices: 22930344--22930377 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
22930334 AGGTATTTGT
22930344 TTTTC TTTTC TTTTC TTTTC TTTT- TATTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTT
22930378 TTGGACCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:22937271 original size:15 final size:16
Alignment explanation
Indices: 22937251--22937283 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22937241 ATTCGATCTC
22937251 AAAAAAAAAGAA-AAG
1 AAAAAAAAAGAAGAAG
*
22937266 AAAAAAGAAGAAGAAG
1 AAAAAAAAAGAAGAAG
22937282 AA
1 AA
22937284 GCAAAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAG
Found at i:22937341 original size:40 final size:40
Alignment explanation
Indices: 22937279--22937382 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 40
22937269 AAAGAAGAAG
* * *
22937279 AAGAAGCAAAA-ACAAAAGCAAAAT-CAAGATCAAAACAAAA
1 AAGAAGAAAAAGA-AAAAGCAAAATAAAAAATCAAAA-AAAA
* *
22937319 AAGAAGAAAAAGAAAAATCAAAATAAAAAATCAAAATAAA
1 AAGAAGAAAAAGAAAAAGCAAAATAAAAAATCAAAAAAAA
*
22937359 ATGAGAGAAAAAGAAAGAAG-AAAA
1 AAGA-AGAAAAAGAAA-AAGCAAAA
22937383 GAAGAAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 26 0.49
41 25 0.47
42 2 0.04
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.07
Consensus pattern (40 bp):
AAGAAGAAAAAGAAAAAGCAAAATAAAAAATCAAAAAAAA
Found at i:22937346 original size:12 final size:12
Alignment explanation
Indices: 22937326--22937359 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
22937316 AAAAAGAAGA
*
22937326 AAAAGAAAAATC
1 AAAATAAAAATC
22937338 AAAATAAAAAATC
1 AAAAT-AAAAATC
22937351 AAAATAAAA
1 AAAATAAAA
22937360 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:22937347 original size:13 final size:13
Alignment explanation
Indices: 22937331--22937359 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22937321 GAAGAAAAAG
22937331 AAAAATCAAAATA
1 AAAAATCAAAATA
22937344 AAAAATCAAAATA
1 AAAAATCAAAATA
22937357 AAA
1 AAA
22937360 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:22938273 original size:7 final size:7
Alignment explanation
Indices: 22938257--22938310 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 7
22938247 CTTTGAGTAA
*
22938257 AAAAACG
1 AAAAATG
22938264 AAAAATG
1 AAAAATG
22938271 AAAAAATG
1 -AAAAATG
22938279 -AAAATG
1 AAAAATG
*
22938285 GAAAATG
1 AAAAATG
22938292 AAAAA-G
1 AAAAATG
*
22938298 AAAAGT-
1 AAAAATG
22938304 AAAAATG
1 AAAAATG
22938311 GAGAGGCTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 16 0.41
7 16 0.41
8 7 0.18
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:22939655 original size:44 final size:44
Alignment explanation
Indices: 22939602--22939855 Score: 172
Period size: 44 Copynumber: 5.5 Consensus size: 44
22939592 CGAAGCCAAA
* *
22939602 AATCTTATCTCCTTGAGATTACAGCGGATCAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
* * ** *
22939646 AATCCTATCTCCCTGAGATTACAGTGGAGT-GGATT-AAAATAAAT
1 AATCCTATCTCCCTGAGATTACAGCGGA-TCAGATTGAAGCT-AGT
* * * * * * * *
22939690 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGA
1 AATCCTATCTCCCTGAGA-TTAC--------AG--CGGATCAGATTGAAGCTAGT
* * * *
22939744 AATCTTATCTCCCTGAAATTACAGCGAAGCAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
* *
22939788 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAAT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
*
22939832 AATCCTATCTCCCTAAGATTACAG
1 AATCCTATCTCCCTGAGATTACAG
22939856 TGGAACGGAT
Statistics
Matches: 164, Mismatches: 30, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
43 5 0.03
44 124 0.76
45 1 0.01
46 2 0.01
52 2 0.01
53 1 0.01
54 23 0.14
55 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
Found at i:22940058 original size:50 final size:50
Alignment explanation
Indices: 22939993--22940777 Score: 492
Period size: 50 Copynumber: 15.7 Consensus size: 50
22939983 GTAGTGGAAC
* * * *
22939993 AGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * * * * * ** *
22940043 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
22940093 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *** ** * * * ** ** *
22940143 AGATTAAAGCTACAGTAGCAAATCTTACCTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
22940193 AGATTAAAGCCACAACGGTGAATCTT-GTCTCCCTGACATTGCAGTTGAAA
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTAAAA
* * ** * * * * **
22940243 AGACTAAAGCCACAGC-GACAAGTGTTACTTCCCTGGCAATGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAA-TCTTACTTCCCTGACATTGCAGTTAAAA
* * * *
22940293 AGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * * * * * * * **
22940343 GGATTAAAGTCACAACGATGAATCTCACTCTCTCAGCCAGTACAG-TAGAGC
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTA-AAA
* * * *
22940394 ATATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGCT-AAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * * * * * * ** *
22940443 AGAATTAAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGCAGTGGAAC
1 AG-ATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * *
22940494 AGGTTAAAGCCACAACGGTGAATCTT-GTCTCCCTAACATTGCAGTTGAAA
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTAAAA
* * * * * * * * **
22940544 AGACTAAAGCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
22940594 AGATTAAAGCCACAACGGTAAATCTTGCTTTCCC-GACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * ** * * * *
22940644 GGATTAAAGTCACAACGACGAATCTCAC-TCTCTAAGACAGTGCAG-TAGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCT--GACATTGCAGTTA-AAA
* *
22940695 AGATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * *
22940745 GGATTAAAGCTACAACAGTGAATCTTACTTCCC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCC
22940778 AGGCAGTGCA
Statistics
Matches: 536, Mismatches: 178, Indels: 43
0.71 0.24 0.06
Matches are distributed among these distances:
48 3 0.01
49 15 0.03
50 431 0.80
51 83 0.15
52 1 0.00
53 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
Found at i:22940140 original size:100 final size:100
Alignment explanation
Indices: 22939985--22940810 Score: 908
Period size: 100 Copynumber: 8.2 Consensus size: 100
22939975 CAAACGATGT
* * *
22939985 AGTGGAACAGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
22940050 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
66 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
*
22940085 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
** * *
22940150 AGCTACAGTAGCAAATCTTACCTCCCAGGCGGTGC
66 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* *
22940185 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTG-TCTCCCTGACATTGCAGTTGAAAAGACTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCT-TCCCTGACATTGCAGTTAAAAAGATTA
* * * *
22940249 AAGC--C-ACAGCGACAAGTGTTACTTCCCTGGCAATGC
65 AAGCTACAACAGCG--AA-TCTTACCTCCCAGGCAGTGC
* * * *
22940285 AGT-GAAGCAGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAAGGATTA
1 AGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTA
* * * * *
22940349 AAG-TCACAAC-GATGAATCTCACTCTCTCAGCCAGTAC
65 AAGCT-ACAACAG-CGAATCTTAC-CTCCCAGGCAGTGC
* * * * *
22940386 AGTAGAGCATATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGCT-AAAAGAATT
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAG-ATT
* *
22940449 AAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGC
64 AAAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* * * *
22940486 AGTGGAACAGGTTAAAGCCACAACGGTGAATCTTG-TCTCCCTAACATTGCAGTTGAAAAGACTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCT-TCCCTGACATTGCAGTTAAAAAGATTA
* * * * * *
22940550 AAGCCACAGCAGCGAATGTTACTTCCCTGGCAATGC
65 AAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* *
22940586 AGT-GAAGCAGATTAAAGCCACAACGGTAAATCTTGCTTTCCC-GACATTGCAGTTAAAAGGATT
1 AGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAGATT
* ** *
22940649 AAAG-TCACAAC-GACGAATCTCACTCTCTAAGACAGTGC
64 AAAGCT-ACAACAG-CGAATCTTAC-CTCCCAGGCAGTGC
* * *
22940687 AGTAGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGTTAAAAGGATTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAGATTA
* *
22940751 AAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGC
65 AAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* * *
22940787 AGTGGAACAAATTGAAGCTACAAC
1 AGTGGAACAGATTAAAGCCACAAC
22940811 AACAAATCTC
Statistics
Matches: 607, Mismatches: 90, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
97 3 0.00
98 2 0.00
99 13 0.02
100 409 0.67
101 161 0.27
102 16 0.03
103 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
Found at i:22940535 original size:301 final size:301
Alignment explanation
Indices: 22939992--22940810 Score: 1238
Period size: 301 Copynumber: 2.7 Consensus size: 301
22939982 TGTAGTGGAA
* * * * *
22939992 CAGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAAAG-CTAC
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTC-AC
* * * * *
22940056 AAC-AGCGAATCTTAC-CTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTT
65 AACGA-CGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTT
* ** * * *
22940119 GC-CTCCCTGACATTGCAGTTAAAA-AGATTAAAGCTACAGTAGCAAATCTTACCTCCCAGGCGG
129 GCTTTCCC-GACATTGCAGTTAAAAGA-ATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAG
*
22940182 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTGACATTGCAGTTGAAAAGAC
192 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGAC
22940247 TAAAGCCACAGC-GAC-AAGTGTTACTTCCCTGGCAATGCAGTGAAG
257 TAAAGCCACAGCAG-CGAA-TGTTACTTCCCTGGCAATGCAGTGAAG
* *
22940292 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAAGGATTAAAGTCACA
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
* * * * *
22940357 ACGATGAATCTCACTCTCTCAGCCAGTACAGTAGAGCATATTAAAGCCACATCGGTGAATCTTGC
66 ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
* *
22940422 TTTCCCGACATTGCAGCTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGCA
131 TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
*
22940487 GTGGAACAGGTTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
196 GTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
22940552 GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
261 GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
22940593 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
*
22940658 ACGACGAATCTCACTCTCTAAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
66 ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
* *
22940723 TTTCCCGACATTGCAGTTAAAAGGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCA
131 TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
* * *
22940788 GTGGAACAAATTGAAGCTACAAC
196 GTGGAACAGATTAAAGCCACAAC
22940811 AACAAATCTC
Statistics
Matches: 470, Mismatches: 42, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
300 66 0.14
301 396 0.84
302 8 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (301 bp):
CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
GTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
Found at i:22942985 original size:2 final size:2
Alignment explanation
Indices: 22942978--22943003 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22942968 TCAAACTTTC
22942978 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
22943004 CATTTCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22964058 original size:16 final size:15
Alignment explanation
Indices: 22964025--22964062 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
22964015 GGATTTTAAA
22964025 TTTTTAAAAATAGTT
1 TTTTTAAAAATAGTT
22964040 TTTTTAAAATATA-TAT
1 TTTTTAAAA-ATAGT-T
22964056 TTTTTAA
1 TTTTTAA
22964063 TTTTTAGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAATAGTT
Found at i:22964175 original size:60 final size:61
Alignment explanation
Indices: 22964073--22964189 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
22964063 TTTTTAGTGG
* * * **
22964073 TAGAACTAAATTGATAGATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
1 TAGAAATAAAGTGATAAATTTTGTAAACATTGAGGGCCAAATTTATTAAATTTTTTATAAT
** *
22964134 TAGAAATAAAGTGATAAATTTT-TAAACATTGAGGGTGAAATTTGTTAAATTTTTTA
1 TAGAAATAAAGTGATAAATTTTGTAAACATTGAGGGCCAAATTTATTAAATTTTTTA
22964190 GATTTAGGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 29 0.60
61 19 0.40
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (61 bp):
TAGAAATAAAGTGATAAATTTTGTAAACATTGAGGGCCAAATTTATTAAATTTTTTATAAT
Found at i:22965511 original size:17 final size:18
Alignment explanation
Indices: 22965476--22965529 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
22965466 GTTATTGTTG
*
22965476 TTTATTATATTACTAATTTT
1 TTTATTAT-TTA-TAATATT
22965496 TTTA-T-TTTAT-ATATT
1 TTTATTATTTATAATATT
22965511 TTTATTATTTATAATATT
1 TTTATTATTTATAATATT
22965529 T
1 T
22965530 ATCACGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 8 0.27
18 7 0.23
19 1 0.03
20 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATTTATAATATT
Found at i:22965750 original size:21 final size:20
Alignment explanation
Indices: 22965720--22965764 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
22965710 AAGAAAAGGA
22965720 AAATTAATTACATTA-TTTT
1 AAATTAATTACATTAGTTTT
*
22965739 GAAATTATATTACTTTAGTTTT
1 -AAATTA-ATTACATTAGTTTT
22965761 AAAT
1 AAAT
22965765 GGGAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
AAATTAATTACATTAGTTTT
Found at i:22975091 original size:21 final size:21
Alignment explanation
Indices: 22975058--22975109 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
22975048 AGAAAATGGC
*
22975058 AGCAACAAAATGGTTGAAAAAT
1 AGCAAC-AAATGGGTGAAAAAT
*
22975080 AGCAACAAATGGGTGGAAAAT
1 AGCAACAAATGGGTGAAAAAT
* *
22975101 GGCAGCAAA
1 AGCAACAAA
22975110 GAGGGCCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.13
Consensus pattern (21 bp):
AGCAACAAATGGGTGAAAAAT
Found at i:22975098 original size:22 final size:22
Alignment explanation
Indices: 22975058--22975099 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22975048 AGAAAATGGC
*
22975058 AGCAACAAAATGGTTGAAAAAT
1 AGCAACAAAATGGTGGAAAAAT
22975080 AGCAAC-AAATGGGTGGAAAA
1 AGCAACAAAAT-GGTGGAAAA
22975100 TGGCAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.10, G:0.24, T:0.14
Consensus pattern (22 bp):
AGCAACAAAATGGTGGAAAAAT
Found at i:22975366 original size:20 final size:21
Alignment explanation
Indices: 22975325--22975366 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
22975315 AAAAAGTAAT
*
22975325 AAAGTGAAGAGAAAACGGAAA
1 AAAGTGAAAAGAAAACGGAAA
*
22975346 AAAGTGAAAAGAATA-GGAAA
1 AAAGTGAAAAGAAAACGGAAA
22975366 A
1 A
22975367 GAAAACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.07
Consensus pattern (21 bp):
AAAGTGAAAAGAAAACGGAAA
Done.